1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65
#![warn(missing_docs)] //! **noodles-bam** handles the reading and writing of the BAM (Binary Alignment/Map) file format. //! //! The BAM format contains the same information as SAM (Sequence Alignment/Map), namely a SAM //! header and a list of records. //! //! # Examples //! //! ## Read all records //! //! ```no_run //! # use std::{fs::File, io}; //! use noodles_bam as bam; //! //! let mut reader = File::open("sample.bam").map(bam::Reader::new)?; //! reader.read_header()?; //! reader.read_reference_sequences()?; //! //! for result in reader.records() { //! let record = result?; //! println!("{:?}", record); //! } //! # Ok::<(), io::Error>(()) //! ``` //! //! ## Query records //! //! Querying allows filtering records by region. It requires an associated BAM index (BAI). //! //! ```no_run //! # use std::fs::File; //! use noodles_bam::{self as bam, bai}; //! use noodles_core::Region; //! use noodles_sam as sam; //! //! let mut reader = File::open("sample.bam").map(bam::Reader::new)?; //! let header: sam::Header = reader.read_header()?.parse()?; //! //! let reference_sequences = header.reference_sequences(); //! let index = bai::read("sample.bam.bai")?; //! let region = Region::mapped("sq0", 17711..=28657); //! let query = reader.query(&reference_sequences, &index, ®ion)?; //! //! for result in query { //! let record = result?; //! println!("{:?}", record); //! } //! # Ok::<(), Box<dyn std::error::Error>>(()) //! ``` #[cfg(feature = "async")] mod r#async; pub mod bai; pub mod reader; pub mod record; mod writer; pub use self::{reader::Reader, record::Record, writer::Writer}; #[cfg(feature = "async")] pub use self::r#async::{Reader as AsyncReader, Writer as AsyncWriter}; static MAGIC_NUMBER: &[u8] = b"BAM\x01";